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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.30

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-07-10, 11:27 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        pmultiqc

        pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc

        Experiment Setup

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
        Showing 2/2 rows and 7/7 columns.
        Sample NameMSstats Condition: CTMSstats Condition: CNMSstats Condition: QYMSstats BioReplicateFraction GroupFractionLabel
         
        1        		MixtureUPS10.1fmol1
         
         ↳ RD139_Narrow_UPS1_0_1fmol_inj1        		111
         
         ↳ RD139_Narrow_UPS1_0_1fmol_inj2        		211
         
        2        		MixtureUPS10.25fmol2
         
         ↳ RD139_Narrow_UPS1_0_25fmol_inj1        		311
         
         ↳ RD139_Narrow_UPS1_0_25fmol_inj2        		411

        Summary and HeatMap

        Summary Table

        This table shows the quantms pipeline summary statistics.
        This table shows the quantms pipeline summary statistics.
        Showing 1/1 rows.
        #Peptides Quantified#Proteins Quantified
        5729
        1605

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result.
        Including Sample Name, Possible Study Variables, identified the number of peptide in the pipeline, and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the `remove_decoy` parameter.
        Showing 2/2 rows and 8/8 columns.
        Sample NameMSstats Condition: CTMSstats Condition: CNMSstats Condition: QYFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
         
        1        		MixtureUPS10.1fmol
         
         ↳ RD139_Narrow_UPS1_0_1fmol_inj1        		1
        5407
        5407
        871
        1552
         
         ↳ RD139_Narrow_UPS1_0_1fmol_inj2        		1
        5434
        5434
        880
        1562
         
        2        		MixtureUPS10.25fmol
         
         ↳ RD139_Narrow_UPS1_0_25fmol_inj1        		1
        5572
        5572
        901
        1578
         
         ↳ RD139_Narrow_UPS1_0_25fmol_inj2        		1
        5558
        5558
        896
        1588

        Identification Summary

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in quantms pipeline final result
        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
        Created with MultiQC

        ProteinGroups Count

        Number of protein groups per raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
        Created with MultiQC

        Peptide ID Count

        Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), or DIA-NN report files.
        Created with MultiQC

        Modifications Per Raw File

        Compute an occurence table of modifications (e.g. Oxidation (M)) for all peptides, including the unmodified.
        Post-translational modifications contained within the identified peptide sequence.
        Created with MultiQC

        Quantification Analysis

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mainly the mzTab file).
        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms. * BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets. * Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored. * Peptide intensity in each condition (Eg. `CT=Mixture;CN=UPS1;QY=0.1fmol`): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.
        Showing 50/50 rows and 6/6 columns.
        PeptideIDProtein NamePeptide SequenceBest Search ScoreAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        1
        TOLA_ECOLI
        AAAEADDIFGELSSGK
        1.0000
        5.9278
        5.8889
        5.9636
        2
        G3P2_ECOLI
        AAAENIIPHTTGAAK
        1.0000
        5.8269
        5.7804
        5.8688
        3
        RLMH_ECOLI
        AAAEQSWSLSALTLPHPLVR
        1.0000
        6.2390
        6.1953
        6.2787
        4
        PDXJ_ECOLI
        AAAEVGAPFIEIHTGCYADAK
        0.9997
        5.4008
        5.4976
        5.2760
        5
        RL10_ECOLI
        AAAFEGELIPASQIDR
        1.0000
        8.2489
        8.2045
        8.2892
        6
        YFGM_ECOLI
        AAAQLQQGLADTSDENLK
        1.0000
        6.3880
        6.3969
        6.3789
        7
        YFGM_ECOLI
        AAAQLQQGLADTSDENLKAVINLR
        1.0000
        6.1712
        6.0321
        6.2764
        8
        RHLE_ECOLI
        AAATGEALSLVCVDEHK
        1.0000
        5.7073
        5.6799
        5.7331
        9
        SYP_ECOLI
        AAATQEMTLVDTPNAK
        1.0000
        6.2840
        6.2035
        6.3518
        10
        EUTL_ECOLI
        AACNAFTDAVLEIAR
        1.0000
        5.6299
        5.6044
        5.6541
        11
        ACRB_ECOLI
        AADGQMVPFSAFSSSR
        1.0000
        6.0764
        5.9387
        6.1808
        12
        YIDA_ECOLI
        AADGSTVAQTALSYDDYR
        0.9998
        5.6988
        5.6826
        5.7144
        13
        ADHE_ECOLI
        AADIVLQAAIAAGAPK
        1.0000
        7.3764
        7.3461
        7.4048
        14
        NARG_ECOLI
        AADLVDALGQENNPEWK
        1.0000
        5.6929
        5.6454
        5.7357
        15
        DNAK_ECOLI
        AADNKSLGQFNLDGINPAPR
        0.9998
        5.5334
        5.4957
        5.5510
        16
        OXYR_ECOLI
        AADSCHVSQPTLSGQIR
        1.0000
        6.2817
        6.2485
        6.3126
        17
        TALA_ECOLI
        AAEELEKEGINCNLTLLFSFAQAR
        1.0000
        6.2640
        6.2059
        6.3153
        18
        HEMY_ECOLI
        AAELAGNDTIPVEITR
        0.9999
        6.4392
        6.4256
        6.4523
        19
        SYL_ECOLI
        AAENNPELAAFIDECR
        1.0000
        6.6836
        6.6402
        6.7231
        20
        TALB_ECOLI
        AAEQLEKEGINCNLTLLFSFAQAR
        1.0000
        6.9806
        6.8963
        7.0512
        21
        MBHM_ECOLI
        AAESALNIDVPVNAQYIR
        1.0000
        6.1335
        6.1304
        6.1366
        22
        DNAG_ECOLI
        AAESGVSRPVPQLKR
        0.9999
        5.1143
        4.9585
        5.2288
        23
        HDFR_ECOLI
        AAESLYLTQSAVSFR
        1.0000
        5.7540
        5.7105
        5.7935
        24
        RNE_ECOLI
        AAESRPAPFLIHQESNVIVR
        1.0000
        6.5752
        6.5572
        6.5925
        25
        HFLK_ECOLI
        AAFDDAIAARENEQQYIR
        1.0000
        5.8013
        5.6354
        5.9210
        26
        AROF_ECOLI
        AAFPLSLQQEAQIADSR
        1.0000
        5.9273
        5.9306
        5.9241
        27
        AROF_ECOLI
        AAFPLSLQQEAQIADSRK
        0.9998
        5.7612
        5.7318
        5.7887
        28
        BOLA_ECOLI
        AAFQPVFLEVVDESYR
        1.0000
        6.4279
        6.4107
        6.4444
        29
        CLPB_ECOLI
        AAGATTANITQAIEQMR
        1.0000
        5.9836
        5.9726
        5.9908
        30
        YBIS_ECOLI
        AAGEPLPAVVPAGPDNPMGLYALYIGR
        1.0000
        5.9628
        5.8381
        6.0596
        31
        SDHA_ECOLI
        AAGLHLQESIAEQGALR
        1.0000
        5.4225
        5.4295
        5.4154
        32
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGK
        0.9998
        5.1833
        5.1162
        5.2413
        33
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGKK
        1.0000
        5.8222
        5.7763
        5.8638
        34
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVR
        1.0000
        6.4683
        6.5168
        6.4137
        35
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVRK
        0.9998
        6.8321
        6.7758
        6.8819
        36
        ENO_ECOLI
        AAGYELGKDITLAMDCAASEFYK
        1.0000
        6.6467
        6.6291
        6.6636
        37
        YEBE_ECOLI
        AAHQDEPQFGAQSTPLDER
        0.9998
        5.6491
        5.6220
        5.6746
        38
        RIBB_ECOLI
        AAIADGAKPSDLNRPGHVFPLR
        1.0000
        6.4630
        6.4313
        6.4926
        39
        DEOC_ECOLI
        AAIAYGADEVDVVFPYR
        1.0000
        6.7499
        6.6917
        6.8012
        40
        IDH_ECOLI
        AAIEYAIANDRDSVTLVHK
        1.0000
        6.2872
        6.2689
        6.3048
        41
        DPO1_ECOLI
        AAINAPMQGTAADIIKR
        0.9998
        5.8750
        5.8517
        5.8972
        42
        SYFA_ECOLI
        AAISQASDVAALDNVR
        1.0000
        6.5821
        6.5777
        6.5864
        43
        SYFA_ECOLI
        AAISQASDVAALDNVRVEYLGK
        1.0000
        6.0451
        5.9836
        6.0990
        44
        MUKF_ECOLI
        AAISSCELLLSETSGTLR
        0.9998
        5.4539
        5.3950
        5.5057
        45
        MSCM_ECOLI
        AAKPAQPEVVEALQSALNALEER
        0.9999
        5.2647
        5.1693
        5.3428
        46
        AMPN_ECOLI
        AALEQLKGLENLSGDLYEK
        1.0000
        6.2583
        6.1947
        6.3138
        47
        DBHA_ECOLI
        AALESTLAAITESLK
        1.0000
        7.0020
        7.0119
        6.9919
        48
        HEM3_ECOLI
        AALPPEISLPAVGQGAVGIECR
        0.9999
        6.3107
        6.2797
        6.3396
        49
        SDHA_ECOLI
        AALQISQSGQTCALLSK
        0.9999
        5.5633
        5.4781
        5.6344
        50
        DHE4_ECOLI
        AANAGGVATSGLEMAQNAAR
        1.0000
        5.7321
        5.6606
        5.7934

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mainly the mzTab file).
        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run. * Peptides_Number: The number of peptides for each protein. * Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored. * Protein intensity in each condition (Eg. `CT=Mixture;CN=UPS1;QY=0.1fmol`): Summarize intensity of peptides.
        Showing 50/50 rows and 5/5 columns.
        ProteinIDProtein NameNumber of PeptidesAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        1
        3PASE_ECOLI
        1
        5.6235
        5.6046
        5.6415
        2
        5DNU_ECOLI
        1
        5.1934
        5.1118
        5.2621
        3
        6PGD_ECOLI
        10
        7.4306
        7.4143
        7.4446
        4
        6PGL_ECOLI
        2
        6.5057
        6.4721
        6.5331
        5
        AAEB_ECOLI
        1
        6.1800
        6.1410
        6.2158
        6
        AAS_ECOLI
        4
        6.0912
        6.0728
        6.0645
        7
        AAT_ECOLI
        2
        7.1735
        7.1515
        7.1944
        8
        ABGT_ECOLI
        1
        5.2444
        5.3301
        5.1374
        9
        ACCA_ECOLI
        10
        7.5188
        7.4724
        7.5607
        10
        ACCC_ECOLI
        11
        7.5447
        7.5080
        7.5786
        11
        ACCD_ECOLI
        4
        6.9568
        6.9438
        6.9695
        12
        ACEA_ECOLI
        10
        7.0495
        7.0004
        7.0936
        13
        ACFD_ECOLI
        8
        6.8296
        6.7905
        6.8657
        14
        ACKA_ECOLI
        9
        8.1525
        8.1204
        8.1816
        15
        ACNA_ECOLI
        5
        6.1236
        6.0315
        6.1795
        16
        ACNB_ECOLI
        11
        7.4528
        7.4149
        7.4828
        17
        ACRA_ECOLI
        6
        7.4974
        7.4509
        7.5394
        18
        ACRB_ECOLI
        6
        6.7660
        6.6959
        6.8263
        19
        ACSA_ECOLI
        2
        5.6039
        5.6355
        5.5511
        20
        ACUI_ECOLI
        5
        7.0524
        6.9583
        7.1097
        21
        ACYP_ECOLI
        1
        5.6173
        5.6039
        5.6238
        22
        ADD_ECOLI
        5
        7.1199
        7.1375
        7.1068
        23
        ADEC_ECOLI
        1
        5.3880
        5.3527
        5.4207
        24
        ADHE_ECOLI
        33
        8.5391
        8.4942
        8.5798
        25
        ADHP_ECOLI
        2
        5.8313
        5.8293
        5.8333
        26
        ADIA_ECOLI
        3
        5.9251
        5.8502
        5.9848
        27
        ADPP_ECOLI
        2
        6.3923
        6.3622
        6.4204
        28
        AGP_ECOLI
        3
        6.1377
        6.1064
        6.1668
        29
        AHPC_ECOLI
        9
        7.9186
        7.8892
        7.9463
        30
        AHPF_ECOLI
        9
        7.4292
        7.4037
        7.4533
        31
        AHR_ECOLI
        1
        5.0382
        5.1352
        4.9801
        32
        AK1H_ECOLI
        7
        6.4884
        6.4593
        6.5158
        33
        AK2H_ECOLI
        4
        6.5019
        6.4721
        6.5298
        34
        AK3_ECOLI
        5
        6.6134
        6.5366
        6.6421
        35
        ALAA_ECOLI
        3
        6.6067
        6.5814
        6.6305
        36
        ALAC_ECOLI
        5
        6.4739
        6.4394
        6.5059
        37
        ALDB_ECOLI
        1
        6.0428
        6.0105
        6.0729
        38
        ALF1_ECOLI
        2
        5.7993
        5.0883
        5.8061
        39
        ALF_ECOLI
        10
        7.9717
        7.9422
        7.9992
        40
        ALKH_ECOLI
        3
        6.6459
        6.5686
        6.7115
        41
        ALR1_ECOLI
        3
        6.6652
        6.6304
        6.6974
        42
        AMIA_ECOLI
        1
        5.8082
        5.7658
        5.8469
        43
        AMIB_ECOLI
        2
        5.7290
        5.6933
        5.7621
        44
        AMIC_ECOLI
        5
        5.9764
        5.8423
        6.0306
        45
        AMID_ECOLI
        1
        4.6107
        4.3583
        4.6972
        46
        AMN_ECOLI
        8
        6.7648
        6.7423
        6.7877
        47
        AMPA_ECOLI
        7
        7.1145
        7.0752
        7.1505
        48
        AMPC_ECOLI
        2
        6.1201
        6.0621
        6.1713
        49
        AMPH_ECOLI
        2
        6.1563
        6.0922
        6.2121
        50
        AMPN_ECOLI
        7
        7.0764
        7.0526
        7.0991

        Intensity Distribution

        log2(Precursor.Normalised) for each Run.
        [DIA-NN: report.tsv] log2(Precursor.Normalised) for each Run.
        Created with MultiQC

        Standard Deviation of Intensity

        Standard deviation of intensity under different experimental conditions.
        [DIA-NN: report.tsv] First, identify the experimental conditions from the "Run" name. Then, group the data by experimental condition and Modified.Sequence, and calculate the standard deviation of log2(Precursor.Normalised).
        Created with MultiQC

        MS2 and Spectral Stats

        Charge-state of Per File

        The distribution of the charge-state of the precursor ion.
        [DIA-NN: report.tsv] The distribution of the charge-state of the precursor ion (Precursor.Charge).
        Created with MultiQC

        MS/MS Counts Per 3D-peak

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.
        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.
        Created with MultiQC

        nf-core/quantms Software Versions

        nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT sdrf-pipelines 0.0.21
        DIANNSUMMARY DIA-NN 1.8.1
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MSSTATS bioconductor-msstats 4.2.0
        r-base 4.1.2
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        Core Nextflow options

        runName
        voluminous_thompson
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_dia,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
        outdir
        ./results_dia

        Protein database

        database
        /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_precursor_charge
        3
        min_peptide_length
        15
        max_peptide_length
        30
        max_mods
        2

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8
        min_pr_mz
        350
        max_pr_mz
        950
        min_fr_mz
        500
        max_fr_mz
        1500
        diann_normalize
        N/A

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DIA
        config_profile_description
        Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.